Virtual Outcrops Building in Extreme Logistic Conditions for Data
Collection, Geological Mapping, and Teaching: The Santorini’s
Caldera Case Study, Greece
Fabio Luca Bonali
1,2 a
, Luca Fallati
1b
, Varvara Antoniou
3c
, Kyriaki Drymoni
4d
,
Federico Pasquaré Mariotto
5e
, Noemi Corti
1f
, Alessandro Tibaldi
1,2 g
, Agust Gudmundsson
4
and Paraskevi Nomikou
3h
1
Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 4,
Ed. U04, 20126, Milan, Italy
2
CRUST- Interuniversity Center for 3D Seismotectonics with Territorial Applications, Italy
3
Department of Geology and Geoenvironment, National and Kapodistrian University of Athens,
Panepistimioupoli Zografou, 15784 Athens, Greece
4
Department of Earth Sciences, Queen's Building, Royal Holloway University of London, Egham, Surrey TW20 0EX, U.K.
5
Department of Human and Innovation Sciences, Insubria University, Via S. Abbondio 12, 22100 Como, Italy
Kyriaki.Drymoni.2015@live.rhul.ac.uk, n.corti3@campus.unimib.it, pas.mariotto@uninsubria.it,
Agust.Gudmundsson@rhul.ac.uk
Keywords: Virtual Outcrops, Photogrammetry, Structure from Motion, Santorini Volcano, Caldera, Dykes.
Abstract: In the present work, we test the application of boat-camera-based photogrammetry as a tool for Virtual
Outcrops (VOs) building on geological mapping and data collection. We used a 20 MPX camera run by an
operator who collected pictures almost continuously, keeping the camera parallel to the ground and opposite
to the target during a boat survey. Our selected target was the northern part of Santorini’s caldera wall, a
structure of great geological interest. A total of 887 pictures were collected along a 5.5-km-long section along
an almost vertical caldera outcrop. The survey was performed at a constant boat speed of about 4 m/s and a
coastal approaching range of 35.8 to 296.5m. Using the Structure from Motion technique we: i) produced a
successful and high-resolution 3D model of the studied area, ii) designed high-resolution VOs for two selected
caldera sections, iii) investigated the regional geology, iv) collected qualitative and quantitative structural data
along the vertical caldera cliff, and v) provided a new VO building approach in extreme logistic conditions.
1 INTRODUCTION
Field studies and data collection are vital components
for geological mapping and for understanding the
active processes on Earth, with particular regard to
shallow magmatic ones (e.g. Tibaldi and Bonali,
2017; Gudmundsson, 2020). Field studies can be
a
https://orcid.org/0000-0003-3256-0793
b
https://orcid.org/0000-0002-5816-6316
c
https://orcid.org/0000-0002-5099-0351
d
https://orcid.org/0000-0001-7262-8719
e
https://orcid.org/0000-0003-2157-8760
f
https://orcid.org/0000-0002-0798-6429
g
https://orcid.org/0000-0003-2871-8009
h
https://orcid.org/0000-0001-8842-9730
challenging, due to particular field-related conditions,
that cause limited outcrop accessibility and result in
poor data collection.
Thus, mapping and data collection on Unmanned
Aerial Vehicles (UAVs)-based photogrammetry-
derived Digital Surface Models (DSMs),
Orthomosaics and Virtual Outcrops (VOs), have
become standard practice, especially in volcanic areas
Bonali, F., Fallati, L., Antoniou, V., Drymoni, K., Mariotto, F., Corti, N., Tibaldi, A., Gudmundsson, A. and Nomikou, P.
Virtual Outcrops Building in Extreme Logistic Conditions for Data Collection, Geological Mapping, and Teaching: The Santorini’s Caldera Case Study, Greece.
DOI: 10.5220/0010419300670074
In Proceedings of the 7th Inter national Conference on Geographical Information Systems Theory, Applications and Management (GISTAM 2021), pages 67-74
ISBN: 978-989-758-503-6
Copyright
c
2021 by SCITEPRESS Science and Technology Publications, Lda. All rights reserved
67
(e.g. Bonali et al., 2020; Tibaldi et al., 2020). VOs are
also known as digital outcrop models, which are a
digital 3D representation of the outcrop surface (e.g
Xu et al., 1999). By contrast, static camera-based
outcomes are rare and restricted to narrow-sized
surveys on small field-scale geological features (e.g.
Scott et al., 2020).
In this paper, we test the use of camera-based
photogrammetry for reconstructing the northern part
of Santorini’s caldera wall (Fig. 1) for subsequent
geological studies. The wall represents an outstanding
vertical outcrop of layered deposits dissected by a
well-exposed local dyke swarm (Figs. 2a-b). It is
characterized by extreme logistic conditions
preventing efficient field and UAV surveys due to its
steepness and elevation (max height of 330 m a.s.l.).
2 GEOLOGICAL BACKGROUND
The Santorini Volcanic Complex is located in the
Aegean Sea and represents the westernmost part of
the active Greek volcanic arc (Le Pichon and
Angelier, 1979). It is an active stratovolcano
composed of five islands (Fig. 1) that were initially
united, before multiple (at least four) caldera collapse
events formed the currently flooded caldera
morphology (Druitt, 2014) (e.g. Fig. 2a).
Figure 1: Satellite view of Santorini volcanic complex; the
major islands and volcanotectonic lineaments are shown
(CSK - Christiana-Santorini-Kolumbo).
Previous studies (Druitt et al., 1999; Rizzo et al.,
2015; Hooft et al., 2017) suggest the existence of
three volcanotectonic lineaments (Kameni line,
Kolumbo line and the Christiana-Santorini-Kolumbo
rift zone) which dissect the island and control magma
ascent in the shallow crust. Although volcanic
activity has been ceased since 1950, the 2011-2012
unrest episode showed magma accumulation beneath
the Nea Kameni island (Parks et al., 2012) while the
intense seismic activity along the Kameni V-T line
exhibited a possible resurgence which, however, did
not fed an eruption (Browning et al., 2015). The
stratigraphy of the northern part of the caldera wall
indicates a large sequence of effusive/explosive
subaerial volcanic activity with a variety of volcanic
products, and in particular lavas, scoria, tuffs and
hyaloclastites (Druitt et al., 1999) (Fig. 2b).
Figure 2: (A) View of the northern caldera wall; the Oia
village, as well as Mt Megalo and Kokkino Vouno, are
highlighted. (B) Dykes dissect the heterogeneous host rock.
Av1 unit: andesitic lavas, tuffs, breccia, and hyaloclastites.
Av3 unit: thinly bedded andesitic and basaltic lavas with
subordinate dacites, tuffs and scoria.
The basement lithologies belong to the Peristeria
stratovolcano (active 530-430 ka) and are capped by
the products of two later explosive cycles (360-3.6
ka). The Minoan Plinian eruption ignimbrite lies atop.
The dyke-fed eruptions are attested by a local radial
dyke swarm of 90 segments that are visible on the
caldera wall and reflect the magmatic and
volcanotectonic evolution of the volcano’s plumbing
system (Drymoni, 2020). The dykes follow variable
paths, and many cross-cutting relationships are
observed. Many arrested, deflected, and feeder-dykes
GISTAM 2021 - 7th International Conference on Geographical Information Systems Theory, Applications and Management
68
occur and dissect dissimilar mechanically layers
(Drymoni et al., 2020).
3 3D MODELLING
In this section, we describe the workflow through
which we applied the SfM techniques (e.g. Westoby
et al., 2012; Pepe and Prezioso, 2016; Bliakharskii
and Florinsky, 2018), which is subdivided into two
main steps: i) Boat survey and picture collection; and
ii) SfM photogrammetry processing. The final results
are provided in the form of VOs, DSMs, and an
Orthomosaic.
3.1 Boat Survey and Picture Collection
Instead of using a commercial UAV, we collected 887
pictures using a static camera, the Sony HX400V
bridge model, equipped with the Sensor CMOS
Exmor 1/2.3" (7.82 mm), 20.4 megapixel,
capable of providing GPS tagged photos (Geographic
coordinates/Datum WGS84), camera lens ZEISS
Vario-Sonna T* and φ55. The operator took the
pictures by keeping the camera parallel to the
“ground” and opposite to the caldera wall. Adjusted
camera settings were used, such as a Sport capture
mode and a constant focal length set to 4.34 mm. The
boat navigated along a 5.5 km track parallel to the
caldera wall from the W to the E-ESE, keeping a
constant speed of 4m/s (Fig. 3). The duration of the
boat survey was 25 mins, and the horizontal distance
range from the coastline was between 35.8 and 296.5
m (Fig. 3), with an average of 144.1 m (SD=70 m).
The Z value of each picture was corrected to a value
of 4.5 m a.s.l, resulting from GPS Real-time
kinematic (RTK) data recording.
Figure 3: Location of the collected pictures, with their
distance from the coast classified in 50m-length intervals.
The red curve highlights the area of interest, the boat track
is indicated by black arrows.
3.2 Photogrammetry Processing
The workflow continued with photogrammetry
processing. All pictures were managed through the
Agisoft Metashape (http://www.agisoft.com/)
photogrammetric software, which processes digital
images and generates 3D spatial data, providing a
high quality of point clouds (Burns et al., 2017). At a
general level, we followed the workflow used in
Bonali et al. (2020): i) picture alignment and sparse
cloud generation; ii) dense cloud building; iii) VO,
DSM and Orthomosaic generation. Firstly, the
pictures were uploaded and edited individually to
mask all the areas external to the caldera wall (sky
and sea) (Fig. 4), to achieve a better processing.
Figure 4: Masked picture; some commonly recognised
points by the software are also shown.
The next step consisted in getting an initial low-quality
photo alignment by considering only the measured
camera locations. Eventually, all the photos with
quality value ˂ 0.8 (or out of focus - visual revision)
were excluded from any further processing. To allow
for the co-registration of datasets and the calibration of
models resulting from SfM photogrammetry
processing, we added 50 Ground Control Points
(GCPs), (e.g. Westoby et al., 2012; James et al., 2017),
all provided with 1 m of accuracy. We considered the
latitude and longitude values from georeferenced aerial
photos and the elevation values from previous high-
resolution models designed by the National and
Kapodistrian University of Athens. After this step, we
re-processed the alignment to obtain better quality.
Regarding the alignment, we tested a total of 16
different approaches, considering the following
features: i) High and Medium accuracy; ii) Generic
and/or Reference preselection, as well as none of them;
iii) Key/Tie Point limit set to 40,000/4,000 and
100,000/10,000 respectively. For each, the dense cloud
Virtual Outcrops Building in Extreme Logistic Conditions for Data Collection, Geological Mapping, and Teaching: The Santorini’s Caldera
Case Study, Greece
69
was generated with Medium accuracy and Mild depth
filtering. After these steps, we selected the most
efficient approach, considering the overall total length
of the processing time and the number of points of the
produced dense cloud. The most efficient approach to
generate the dense cloud was finally found to be the
Alignment with Medium accuracy and both Generic
and Reference selection activated (Fig. 5); the pictures
overlap ratio is always greater than 90%.
Figure 5: Graph showing the processing time vs the number
of dense cloud points, for the 16 different processing
approaches.
The duration of the aforementioned step was 121
mins, and the produced dense cloud had 63,770,936
points. Processing was performed using the Agisoft
Cloud beta service, from a virtual machine equipped
with the following features: a CPU-32 vCPU (2.7
GHz Intel Xeon E5 2686 v4), a GPU 2 × NVIDIA
Tesla M60, a RAM 240 GB. We also applied the
“Filter by Confidence” tool to remove noisy points
from the dense cloud. Primarily, we removed all the
points from the overall dense cloud in the range
between 0–1 and took out the ones which did not
relate to the final area and the model we wished to
obtain. On the resulting dense cloud, composed of
56,961,232 Points (Fig. 6), we first generated the
DSM model, where the Projection was set up to
WGS84 / UTM zone 35N, with interpolation both set
to disabled and enabled. Finally, we assigned the
Orthomosaic feature with the following “Average
setting” as Blending mode, and we kept the “Enable
hole filling” disabled, instead of the “Mosaic” as it is
usually done with UAV-captured pictures.
3.3 VOs Building
Regarding the VOs and the 3-D produced models, the
overall model was built as a tiled model with a Tile
size of 4096x4096 pixels and a medium face count.
This was suggested by Tibaldi et al. (2020), who
proposed to use the Tiled Model as a Virtual Reality
scenario. Some parts were also selected and shared
online for further dissemination activities. In detail, to
create VOs of adequate quality for online sharing, we
suggest the following steps. The first step is to build
the mesh from the dense cloud, with an Arbitrary 3D
surface type, and 2,100,000 number of faces.
Afterwards, it is necessary to create the texture, in two
separated files, with a tile size of 4096x4096 pixels;
then, the 3-D model can be exported in Collada file
format. The output is composed of three files, one for
the mesh (DAE file extension) and two for the texture
(jpg file extension) (Fig. 7a). The online shared model
is shown in Figure 7b.
Figure 6: Best sparse and dense cloud obtained with the
workflow mentioned above, including a “Filter by
confidence” tool.
Figure 7: (A) DAE file for the mesh and the two JPG files
of the texture feature needed for the 3D model (B). Av3 and
Av1 units as well as the dykes and the observed crustal
segment are explained in detail in the caption of Figure 2.
4 RESULTS
4.1 DSMs and Orthomosaic
We collected a total number of 877 pictures to be used
during the photogrammetry processing to build up the
DSM and the Orthomosaic. The size of the research
GISTAM 2021 - 7th International Conference on Geographical Information Systems Theory, Applications and Management
70
area was measured with the ArcGIS Pro tools and was
found to cover 1.84 km
2
(Fig. 3). The DSM,
processed without using interpolation settings,
covered an area of 1.25 km
2
, that is 30 % smaller than
the target area, resulting in a resolution of 22.3 cm/pix
and an elevation range from -2.68 to 311.77 m a.s.l.
(Fig. 8a). The DSM processed using interpolation
settings had the same pixel size, covered the entire
target area, and showed an elevation range from -3.0
to 314.5 m a.s.l. (Fig. 8b). The processing time of the
two DSMs was 3 mins and 22 mins, respectively.
Figure 8: DSMs derived by photogrammetry processing
limited to the target area (red area), built without (A) and
with interpolation settings selected (B).
Figure 9: Orthomosaic derived by photogrammetry
processing restricted to the target area (red area).
The 5-m-resolution DEM provided by the
National Cadastre & Mapping Agency S.A. is in the
range of 2.20 - 329.23 m a.s.l.. Regarding the
Orthomosaic, it has the same areal coverage as the
first DSM, no interpolation settings were selected,
and has a resolution of 5.8 cm/pix (Fig. 9). Its
processing time was 493 mins. To define the research
area, we first calculated a ridgeline. We used the 5-m-
resolution digital elevation model (DEM) derived
from the area's orthophoto map (2012) of the National
Cadastre & Mapping Agency S.A. in ArcGIS Pro, to
create the flow direction initially and then the flow
accumulation raster files by applying the DINF
method, that uses the steepest slope of a triangular
facet. Then, we reclassified the flow accumulation
file into two classes separating the zero value areas
from the rest, isolating the ridgeline area. We then
converted the reclassified raster file to a vector one,
creating the required ridgeline. Finally, using the
orthophoto map of the area, we modified the ridgeline
as well as the coastline excluding the residential
areas.
4.2 3-D Tiled Model and VOs
We produced the overall 3D Tiled model in 270 mins,
and the texture resolution was similar to the
Orthomosaic value, i.e. 5.8 cm/pix (Fig. 10a).
Similarly to the DSMs and the Orthomosaic, in terms
of planar areal extent, the covered area is the same.
However, differently from the Orthomosaic and the
DSMs, in the 3D Tiled Model all the vertical parts of
the caldera, which could be mapped on 2D models,
are very well represented, as shown in detail in Figs.
10b-c and from the VO displayed in Figure 7b.
4.3 Relationship between Camera
Location and the Derived Models
Even though this is a first approach, our models
generally showed a positive correlation between the
operator-coast distance and the most representative
elevation values in the derived DSM (no interpolation
- Fig. 8a). However, in the western and southeastern
part of the caldera, the images were collected from a
longer distance, so the elevation values were
portrayed in a better way (both in terms of their areal
coverage and maximum elevation) in the produced
DSM and complied with specific conditions. These
conditions allowed us to estimate the most
representative operator-coast distance vs best-
performed elevation above sea level solutions which
were: i) for ≤100m operator-coast distance, elevation
values were between 0-60m, ii) for 100-200m
Virtual Outcrops Building in Extreme Logistic Conditions for Data Collection, Geological Mapping, and Teaching: The Santorini’s Caldera
Case Study, Greece
71
operator-coast distance, a maximum elevation of 150-
200m could be reached, iii) for >200m operator-coast
distance the elevation values could be suitable for the
whole model (313m maximum vertical altitude). The
above specifications are crucial to plan further similar
field campaigns in such extreme conditions.
Therefore, we designed a protocol to preliminarily
describe the relationship between these realistic field
parameters (operator-caldera distance and elevation),
which can still be improved. First, we calculated the
point density of the DSM data. Then, we selected an
upper elevation limit value wherever the derived
density was high (0.02 km
2
;
Fig. 11). This allowed the
model to trace the most representative solutions. We
used such limit as a parameter towards the minimum
net (3D) distance calculation between this upper limit
and the camera, with information sampling each 1 m
along the line (Fig. 11). We show this relationship in
Figure 12, where the Maximum Elevation reachable
(y-axes) is a function of the 3D distance multiplied by
0.4393 minus 1.7881.
Figure 10: (A) The resulting 3D Tiled Model. (B) 3D model
view of the area below Mt Megalo Vouno. The dykes were
emplaced into a heterogeneous and anisotropic host rock,
which belongs to the oldest local volcanic activity
(Peristeria stratovolcano, 530-430 ka), and dissected the
bottom units: i) av1 - a mixture of andesitic lavas, tuffs,
breccias, and hyaloclastites; ii) av2 - silicic andesitic lavas.
(C) 3D model view of the caldera wall at Oia village.
5 DISCUSSION
Here, we critically discuss the application of our
proposed methodological approach to the VOs,
DSMs and Orthomosaic design in extreme conditions
where the use of UAVs is difficult for image
collection. We have designed a safe, user-friendly,
economic and well-developed approach to build up
3D models aimed at overcoming field-related
challenges but, most importantly, tackling the
technical limitations and methodological impact on
the interpretation of the findings, which could not be
addressed by other techniques. Our well-tested
methodology proposes that the resolution produced
by the SfM-derived DSMs and Orthomosaic is well
portrayed and successfully serves the scopes of
geological interpretation and quantitative and
qualitative data collection for geoscientists.
Figure 11: Map showing the point density values calculated
by the DSM, with no interpolation settings. The blue line
represents the upper elevation selected limit.
We also critically consider that the difference
between the 5-m DSM and the SfM derived model
(interpolation settings were inactive) can produce
good correlations for the used scale (km range) of our
study. Our results show a major difference between
the elevation values produced by the two models (Fig.
13), ranging from -63.19 to 52.32 m, mean value =
-0.09. However, their statistical analysis implies a
much lower standard deviation (SD) value than its
broad range, suggesting instead that the majority of
data are within an SD of 9.95. To obtain results with
a better statistical performance, we propose an
updated scenario which offers: 1) high precision
GCPs, 2) a UAV-based mission in conjunction with
this methodology to complement the collected picture
set considering different cliff and elevation angles.
This can increase the quality of the produced DSM
and provide more accurate structural data. We have
also tested an identical scenario and have designed a
DSM by activating the interpolation settings. The
statistical analysis shows a broader range of values as
well as a greater standard deviation (SD) than in the
previous case; the range is between -62.44 and 98.56,
GISTAM 2021 - 7th International Conference on Geographical Information Systems Theory, Applications and Management
72
the mean is 3.02 and the SD = 13.24 (Fig. 14).
Furthermore, we noticed that both the over and
underestimated elevation values belonged to pictures
collected very close to the coast.
Figure 12: Graph showing the relation between the 3D
distance from the camera and the maximum reachable and
reliable elevation in the DSM.
Figure 13: Raster showing the difference in elevation
between the 5-m DSM and the SfM-derived DSM obtained
with no interpolation settings.
Figure 14: Raster showing the elevation difference between
the 5-m DSM and the SfM-derived DSM obtained with
active interpolation setting.
Finally, although the Orthomosaic suffered from
significant distortion effects due to the high slope
morphology of the target area, the 3D Tiled model, as
well as the selected VOs, show some excellent
vertical outcrops. The above considerations prove
that the proposed technique can be used for research
surveys and data collection protocols; such activities
were once instead impossible to carry out with
sufficient precision, owing to accessibility limitations
(e.g. Fig. 7). For example, our methodology gave
satisfying results in relation to the quantitative
measurements of dyke thickness, as shown in Figs. 2b
and 7. The data of this campaign and especially the
ones related to dyke thickness measured by Drymoni
et al. (2020) in Figs 2b and 7 have been compared
with our derived 3D model, showing excellent
overlap. Similarly, we refer to the comparisons
between another dyke studied by Tibaldi et al. (2020)
and our 3D model. The results show, once again, a
centimetric difference between the two thickness
measurements. Such observations suggest the
practicality, but most importantly the level of
confidence of the SfM-derived 3D models proposed
here, for data collection and 3D geological
reconstructions. Finally, the overall 3D models, as
well as their selected parts, can be excellent teaching
resources and could serve significantly as part of
interactive outreach activities. In this regard, we aim
to enhance the accessibility of the northern caldera
wall, publishing three sites as “Virtual Outcrops”
(e.g. Pasquaré Mariotto et al., 2020) available on the
webpages: https://geovires.unimib.it/geovolc/ and
https://geovires.unimib.it/shallow-magma-bodies/,
where a scientific description is also provided for
each model. Finally, as suggested by Tibaldi et al.
(2020), the SfM-derived 3D Tiled model can be
imported in a game engine, building fully navigable
immersive VR systems (https://www.geavr.eu/).
6 CONCLUSIONS
In the present work, we achieved the following
outcomes: i) a major, high-resolution 3D tiled model
with a texture resolution of 5.8 cm/pix, ii) two DSMs
and an Orthomosaic with a pixel resolution of 22.3
and 5.8 cm/pix respectively, iii) a series of VOs for
dissemination activities. More importantly, we
applied the aforementioned SfM photogrammetry
approach in extreme conditions, providing a
preliminary equation that can be used to plan further
surveys along the almost vertical and inaccessible
cliff, using a static camera to run the pictures
collection task.
Virtual Outcrops Building in Extreme Logistic Conditions for Data Collection, Geological Mapping, and Teaching: The Santorini’s Caldera
Case Study, Greece
73
ACKNOWLEDGEMENTS
Funding is from : i) the ILP-Task Force II (Leader A.
Tibaldi); ii) the MIUR project ACPR15T4_00098–
Argo3D (http://argo3d.unimib.it/); iii) the Virtual
Diver project (https://www.virtualdiver.gr/); iv)
NEANIAS project (https://www.neanias.eu/). Special
thanks to Captain Giorgos Renieris of the Santorini
Boatmen Union. Agisoft Metashape is acknowledged
for photogrammetric data processing. Finally, this
paper is an outcome of GeoVires lab
(https://geovires.unimib.it).
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